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Integrated transcriptome and proteome profiling reveals a set of up-regulated genes/proteins related to low density neutrophils and impairment in transcription and translation processes in clinical sepsis

ABSTRACT: Sepsis is a global health emergency, which is known to be caused by various sources of infection that lead to changes in gene expression, protein coding, and metabolism. Advancements in omics technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. Through integration of transcriptome and proteome profiling, we identified 170 co differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Protein protein interaction network analyses revealed two densely connected regions, which majorly included down regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up regulated genes/proteins, which were mainly related to low density neutrophils (LDNs). IPA analysis revealed enrichment of canonical pathways and diseases or functions annotations, wherein pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. These findings showed a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes related to LDNs and host defense system.

INSTRUMENT(S): Synapt G2 HDMS

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Reinaldo Salomao Alexandre Keiji Tashima

PROVIDER: MSV000087733 | MassIVE | Thu Jul 01 07:38:00 BST 2021

REPOSITORIES: MassIVE

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Project description:Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most destructive bacterial disease of rice. The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races. To identify other genes involved in Xa21-mediated immunity, a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0, 4, 8, 24, 72 and 120 hours post inoculation (hpi) or between incompatible and compatible interactions at 4 hpi, respectively. A total of 441 differentially expressed genes, designated as XDGs (Xa21 mediated Differentially expressed Genes), were identified. Based on their functional annotations, the XDGs were assigned to 14 categories some of which encode resistance/defense related proteins and signaling regulators. Interestingly, most signaling-related genes were down-regulated at 4 and 8 hpi, suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response. Moreover, a number of pathogenesis-related genes were induced at 72 and 120 hpi. Comparison of expression profiles mediated by other resistance genes revealed an interesting common responses in the plant immune system. Comparison analyses also suggest possible overlaps with hormone signaling pathways and with defense systems including basal defense and hypersensitive responses. We investigated the transcriptional characteristics of Xa21-mediated defense responses in rice using whole-genome oligonucleotide microarray, by comparing the expression profiles between incompatible interactions and mock treatments at five time-points and between incompatible and compatible interactions at 4 hours post inoculation. Microarray hybridization at each time point was carried out in three replications including two biological replications and one technological replication. To detect the genes that are significantly regulated and to eliminate those that have inconsistent expression data among replicated experiments, a cutoff of 1.5 fold change and 1.96 for intensity-dependent Z-scores were required in at least two experimental samples.

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Integrated transcriptome and proteome profiling reveals a set of up-regulated genes/proteins related to low density neutrophils and impairment in transcription and translation processes in clinical sepsis

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